5U77 | pdb_00005u77

Crystal structure of ORP8 PH domain

• PDB DOI: https://doi.org/10.2210/pdb5U77/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-11 Released: 2017-10-18 
• Deposition Author(s): Ghai, R., Yang, H.
• Funding Organization(s): NHMRC-ARC dementia research development fellowship, National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.274 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

ORP5 and ORP8 bind phosphatidylinositol-4, 5-biphosphate (PtdIns(4,5)P 2) and regulate its level at the plasma membrane.

Ghai, R., Du, X., Wang, H., Dong, J., Ferguson, C., Brown, A.J., Parton, R.G., Wu, J.W., Yang, H.

(2017) Nat Commun 8: 757-757

• PubMed: 28970484 
• DOI: https://doi.org/10.1038/s41467-017-00861-5
• Primary Citation Related Structures: 
  5U77, 5U78


• PubMed Abstract: 
  

  ORP5 and ORP8, members of the oxysterol-binding protein (OSBP)-related proteins (ORP) family, are endoplasmic reticulum membrane proteins implicated in lipid trafficking. ORP5 and ORP8 are reported to localize to endoplasmic reticulum-plasma membrane junctions via binding to phosphatidylinositol-4-phosphate (PtdIns(4)P), and act as a PtdIns(4)P/phosphatidylserine counter exchanger between the endoplasmic reticulum and plasma membrane. Here we provide evidence that the pleckstrin homology domain of ORP5/8 via PtdIns(4,5)P ₂ , and not PtdIns(4)P binding mediates the recruitment of ORP5/8 to endoplasmic reticulum-plasma membrane contact sites. The OSBP-related domain of ORP8 can extract and transport multiple phosphoinositides in vitro, and knocking down both ORP5 and ORP8 in cells increases the plasma membrane level of PtdIns(4,5)P ₂ with little effect on PtdIns(4)P. Overall, our data show, for the first time, that phosphoinositides other than PtdIns(4)P can also serve as co-exchangers for the transport of cargo lipids by ORPs.ORP5/8 are endoplasmic reticulum (ER) membrane proteins implicated in lipid trafficking that localize to ER-plasma membrane (PM) contacts and maintain membrane homeostasis. Here the authors show that PtdIns(4,5)P ₂ plays a critical role in the targeting and function of ORP5/8 at the PM.

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Organizational Affiliation: 
• School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.
Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, QLD, 4072, Australia.
Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.87 kDa 
• Atom Count: 955 
• Modeled Residue Count: 117 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterol-binding protein-related protein 8	A	123	Homo sapiens	Mutation(s): 0  Gene Names: OSBPL8, KIAA1451, ORP8, OSBP10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZF1 (Homo sapiens) Explore Q9BZF1  Go to UniProtKB:  Q9BZF1
PHAROS:  Q9BZF1 GTEx:  ENSG00000091039

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDB	B [auth A]	N-(2-hydroxyethyl)-N,N-dimethyl-3-sulfopropan-1-aminium C7 H18 N O4 S CNXPCGBLGHKAIL-UHFFFAOYSA-O
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.274 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.079	α = 90
b = 57.079	β = 90
c = 154.949	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Ghai, R., Yang, H.

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Funding Organization	Location	Grant Number
NHMRC-ARC dementia research development fellowship	Australia	1097185
National Health and Medical Research Council (NHMRC, Australia)	Australia	1041301
Australian Research Council (ARC)	Australia	DP130100457

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description